Feeling Sluggish

Somehow, Yeerks are aboard. Yeerks are parasitic brain slugs that slither in through the ear canal of a host, and wrap themselves around the brain, and takes control. The host still acts the same, talks the same, moves the same, but it is the Yeerk. Every three days though, the Yeerk must leave its host and return to the Yeerk Pool to feed on Kandrona rays.
And the Yeerks have a plan. By slowly and quietly infesting the crew and taking control, they plan to get to the brain of Stacey, and make her do what they want, which likely would not involve getting the crew safely back to their own worlds. Only a few of the crew are aware of the threat of the Yeerks...

Sam Winchester, and Connor and Murphy MacManus fell into a strange pool hidden beneath the clockhouse in the City and were infested with Yeerks (parasitic brain slugs that control a host's body).

Sam Winchester infested Xander Harris with a Yeerk.

Lyta Alexander and Ax explored the Labyrinth. Lyta discovered that Ax was an Andalite.

Paco infested Kate Bishop with a Yeerk. They discovered the bathrooms, which were very normal, except for the stall on the end which had a biohazard symbol on it.

Leela Bricker, Lyta Alexander, and Nathan Petrelli explored Escherville. The creepy thing inside of it attacked Leela with visions, and Lyta had to force it out. Leela was infested with a Yeerk while recovering in the MedBay.

Another crew meeting was had, where the known information was shared with the newer crew members and the crew agreed that they needed to learn how to work together to avoid tripping each other up like they had in the fight against the Judas roaches.

West Rosen and Cybil Bennett were both infested with Yeerks at some point.

Brainiac 5 discovered that Ax was not human, and the two of them began working together to build something that would allow them to locate the Kandrona, if any was on board.

Brainy went searching for the Kandrona alone. And found it. He fought briefly with an infested Sam Winchester and Robin, but ultimately lost and was infested as well. The Yeerk was no match for his 12th Level intellect however, and Brainy was able to masquerade as a Controller. Ax witnessed Brainy's infestation, and only barely escaped when Brainy pretended to shoot at him and instead trapped himself, Sam, and Robin in the Pool area. The Yeerks decided that they needed to adjust the time table on their plan.

The Controllers in the crew attacked the free crew, trying to either infest or kill them depending on their known power level. This occasionally backfired (as when one Yeerk tried to infest the Doctor, who countered by going into a healing trance and freezing the Yeerk out), but other times succeeded (Shawn Spencer). Sam’s Yeerk, when cornered, shot Sam in the head. Scorpius seemed to betray the crew by working with the Sub-Visser, but he planned to double-cross him. When he did, Scorpius and the Sub-Visser fought, and the Sub-Visser only barely triumphed by shoving Scorpius into another Pod. He planned to come back for him later.

The Yeerks had located a portion of Stacy’s brain and intended to use some technology they’d located and built to erase portions of her mind and take it over. This would give them control of the ship, and also likely erase any chance the crew had of getting home.

The crew located the Yeerks’ machine. Sub-Visser Seven unleashed an army of hungry Taxxons on them. The crew began to work together to fight the Taxxons, stop the machine from charging up, and take out the Sub-Visser.

The newly Popped crew members encountered Brainy and a few of the others hiding out in the Med Bay. There was a misunderstanding between Superman and Brainy, but it was quickly sorted out. The newly popped Garou (werewolves) went a little nuts, too, but that was also sorted out.

The crew was BAD. ASS. The Yeerks didn't stand a chance. Their machine was destroyed.

The Doctor died and regenerated. Cybil Bennett was revealed to be a Controller, and that her Yeerk was a member of the Yeerk Peace Movement. Her Yeerk then destroyed the Kandrona. Jaime Reyes and Ax had a disagreement about whether they should try to save the Yeerk’s life or not, but the Yeerk was too far gone to save. Cybil put it out of its misery.

Those Yeerks already infesting the crew were starved out. The Sub-Visser revealed with his dying breath that Superboy was going to die.

The crew begins recovering from the Yeerk attack and preparing for the future and their eventual escape from the ship. Command structure is organized.